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Open AccessJournal ArticleDOI

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

Jan O. Korbel, +8 more
- 23 Feb 2009 - 
- Vol. 10, Iss: 2, pp 1-14
TLDR
Paired-End Mapper demonstrated high structural variant reconstruction efficiency for PEMer's coverage-adjusted multi-cutoff scoring-strategy and showed its relative insensitivity to base-calling errors.
Abstract: 
Personal-genomics endeavors, such as the 1000 Genomes project, are generating maps of genomic structural variants by analyzing ends of massively sequenced genome fragments. To process these we developed Paired-End Mapper (PEMer; http://sv.gersteinlab.org/pemer). This comprises an analysis pipeline, compatible with several next-generation sequencing platforms; simulation-based error models, yielding confidence-values for each structural variant; and a back-end database. The simulations demonstrated high structural variant reconstruction efficiency for PEMer's coverage-adjusted multi-cutoff scoring-strategy and showed its relative insensitivity to base-calling errors.

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Citations
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Journal ArticleDOI

DELLY: structural variant discovery by integrated paired-end and split-read analysis

Tobias Rausch, +5 more
- 15 Sep 2012 - 
TL;DR: An SV discovery method that integrates short insert paired-ends, long-range mate-pairs and split-read alignments to accurately delineate genomic rearrangements at single-nucleotide resolution, called DELLY, which enables to ascertain the full spectrum of genomic rearrANGements, including complex events.
Journal ArticleDOI

Genome structural variation discovery and genotyping

Can Alkan, +3 more
- 01 May 2011 - 
TL;DR: It is argued that the long-term goal should be routine, cost-effective and high quality de novo assembly of human genomes to comprehensively assess all classes of structural variation.
Journal ArticleDOI

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

Alexej Abyzov, +3 more
- 01 Jun 2011 - 
TL;DR: By genotyping CNVs in the CEPH, Yoruba, and Chinese-Japanese populations, it is estimated that at least 11% of all CNV loci involve complex, multi-allelic events, a considerably higher estimate than reported earlier.
Journal ArticleDOI

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations

Tobias Rausch, +51 more
- 20 Jan 2012 - 
TL;DR: The whole-genome sequencing-based analysis of a Sonic-Hedgehog medulloblastoma brain tumor from a patient with a germline TP53 mutation is reported, uncovering massive, complex chromosome rearrangements and connecting p53 status and chromothripsis in specific tumor types.
Journal ArticleDOI

De novo assembly and genotyping of variants using colored de Bruijn graphs

Zamin Iqbal, +5 more
- 01 Feb 2012 - 
TL;DR: An efficient software implementation, Cortex, the first de novo assembler capable of assembling multiple eukaryotic genomes simultaneously is provided, and how population information from ten chimpanzees enables accurate variant calls without a reference sequence is shown.
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Journal ArticleDOI

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